'Lithuania would likely have been more energetic in informing the world about an episode of vandalism at its Museum of Genocide Victims' ... Tourists visit the old town of Vilnius. Photograph: Petras Malukas/AFP/Getty Images

In early July the words "Hitler was right" were painted in Russian on the memorial stone to the 72,000 Jews who were murdered at the Ponary Forest near Vilnius in Lithuania. On another monument close by, a vulgar reference was made to the compensation the Lithuanian government has made to the descendants of murdered Jews. No one seems to have noticed.

Vilnius, now the capital of Lithuania, was known for centuries as "the Jerusalem of Lithuania" because of its centrality to medieval and early modern Jewish thought and politics. In the medieval Grand Duchy of Lithuania and the early modern Polish-Lithuanian Commonwealth, Jews settled in Vilnius in considerable numbers from both west and east. Over centuries, Jews prospered under a regime that permitted them local autonomy. During the waning of the commonwealth in the 18th century, Vilnius was home to scholars such as Elijah ben Solomon, the "Gaon of Vilne", the great opponent of the Hasidic movement.

In the 19th century Vilnius was home to the Haskalah, or Jewish Enlightenment, in the Russian Empire. After the first world war, the city was incorporated by Poland, though it was claimed by Lithuania as its capital. There were far more Poles than Lithuanians in the city, but there were about as many Jews as Poles, roughly 80,000 each in the 1920s. In interwar Vilnius, tensions between Poles and Jews and between Poles and Lithuanians were high, but relations between Lithuanians and Jews were relatively peaceful.

In 1939, as the second world war began, the Jews, Poles and Lithuanians of Vilnius fell under Soviet power. By the terms of the Molotov-Ribbentrop pact, the alliance between Nazi Germany and the Soviet Union, eastern Poland (including Vilnius) came within the Soviet sphere of influence. The Soviets in 1939 gave Vilnius to Lithuania, then annexed the whole country in 1940. The NKVD, the Soviet secret police, then set about deporting Lithuania's political and social elites – about 21,000 people in all, including many Jews. Thousands more were shot in NKVD prisons. This level of wartime terror was unprecedented, and its first perpetrators were Soviets rather then Nazis. We remember, for example, that the Japanese diplomat Chiune Sugihara saved several thousand Jews by issuing them transit visas from Lithuania in 1940; what is often overlooked is that these Jews were fleeing not the Holocaust, which had not yet begun, but the threat of Soviet deportations.

Meanwhile, the Germans prepared to betray their Soviet allies. Part of their planning for the invasion of the Soviet Union was the recruitment of local nationalists, who would help them spread their antisemitic message: Nazi rule was liberation from Soviet crimes, which were in fact the fault of local Jews. During the first few weeks of the German invasion, which first touched Lithuania and other lands that the Soviets had just annexed, local peoples took part in a few hundred extremely violent pogroms, killing some 24,000 Jews.

German troops were followed by four Einsatzgruppen, whose task was to murder groups who might resist German power. In Lithuania, more quickly than anywhere else, this mission became mass murder. The Germans' antisemitic equation of Jews with Soviet rule allowed Lithuanians (and others) to find a scapegoat for their own humiliation and suffering under Soviet rule. It also provided an escape route for many who had collaborated with the prior Soviet regime. The Germans had been sheltering Lithuanian nationalists who had fled Soviet rule, and cooperation between German forces and these Lithuanians allowed for a drastic escalation from pogroms to mass shootings.

The mass murder of the Jews of Vilnius could not have taken place without the assistance of Lithuanians: the Germans did not have enough men for the job. That said, it is important to remember that the double occupation of Lithuania, by the Soviets and then by the Germans, was an exceedingly violent break with the previous history of Vilnius and Lithuania. Though the Germans had no trouble finding Lithuanians willing to kill Jews, what happened in 1941 had no precedent in prewar Lithuanian policy or in the history of Lithuanian-Jewish relations.

The German unit assigned to kill the Vilnius Jews was Einsatzkommando 9 of Einsatzgruppe B. By 23 July 1941 the Germans had assembled a Lithuanian auxiliary that marched columns of Jews from Vilnius to the nearby Ponary Forest. Jews were taken in groups of between 12 and 20 to the edge of pits, where they had to hand over valuables and clothes before they were shot. Some 72,000 Jews from Vilnius and elsewhere were murdered at Ponary (as were about 8,000 Poles and Lithuanians). Ita Straż was one of the very few Jewish survivors. She was taken by Lithuanian policemen to a pit full of corpses. The shots missed her, but she fell into the pit, and was covered by the corpses of the people who came after. Later she climbed out and away: "I was barefoot. I walked and walked over corpses. There seemed to be no end to it."

Why has the desecration of such a place escaped our notice? When the "Arbeit macht frei" sign was stolen in late 2009 from the gates of Auschwitz, an international scandal ensued, and the thieves (a Swedish neo-Nazi and two Polish accomplices) were apprehended. Perhaps reporters and editors in western Europe and the US do not associate places like Ponary with the Holocaust. Our imaginations are dominated by Auschwitz, even though more far more Jews were shot at places like Ponary than were murdered in its gas chambers.

For its part, the Lithuanian government tends to focus on the Lithuanian victims of the Soviet occupation. The Germans brought the first Soviet occupation to an end in 1941, but the Red Army returned in 1945, and remained until 1991. Once again thousands of ambitious and able people were deported to Siberia. The Lithuanian political elite matured under Soviet rule. For many Lithuanian politicians, the formative moment of their lives was January 1991, when a special Soviet unit killed 13 Lithuanian protesters. That unit was commanded by Mikhail Golovatov, a KGB officer whom Lithuania now considers a war criminal.

The energies of the Lithuanian government are now focused on his case. Austria had Golovatov in custody on 14 July, but chose to allow him to return to Russia after holding him for less then a day. A leading Austrian opposition politician speaks of his government as having "illegally prostrated itself before Russia". Golovatov himself claims that Russian influence was decisive, though perhaps he simply wishes to worsen Austrian-Lithuanian relations. One of the tenets of Russian foreign policy is to weaken the EU, the better to deal with its member states one by one.

Lithuanian authorities wonder, with justice, whether Lithuania's fellow EU member states understand the difficulties of its Soviet past. The current Lithuanian government thus emphasises Soviet crimes, sometimes to the point of neglecting obvious opportunities to acknowledge the scale of the Holocaust in Lithuania and the role of Lithuanians in the mass shootings on Lithuanian territory. Lithuania would likely have been more energetic in informing the world about an episode of vandalism at its Museum of Genocide Victims, whose exhibitions concern Soviet crimes.

But indubitable western ignorance of Soviet crimes is no excuse for neglecting the historical record of the tragedy of Lithuanian Jews. Horrible as the Soviet occupation was, the largest group of genocide victims in Lithuania were the Jews murdered by the Germans with the help of the local population. These people were, of course, Lithuanian citizens. The responsibility to announce and resolve the crime rests with the Lithuanian authorities, and the local police have accordingly been in contact with the Jewish community of Vilnius (today only some 3,000 people). Aside from basic decency, respect for the history of Lithuania and its peoples would demand that immediate and decisive measures are taken to bring those involved to justice.